Variant report

Variant	rs13064784
Chromosome Location	chr3:49135961-49135962
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TRIM28	chr3:49135852-49136369	K562	blood:	n/a	n/a
2	GABPA	chr3:49135789-49136314	K562	blood:	n/a	n/a
3	POLR2A	chr3:49135787-49136380	K562	blood:	n/a	n/a
4	TEAD4	chr3:49135733-49136329	K562	blood:	n/a	n/a
5	POLR2A	chr3:49135663-49136420	PFSK-1	brain:	n/a	n/a
6	NR2F2	chr3:49135602-49136474	K562	blood:	n/a	n/a
7	STAT5A	chr3:49135623-49135967	GM12878	blood:	n/a	n/a
8	ELF1	chr3:49135838-49136436	K562	blood:	n/a	n/a
9	POLR2A	chr3:49135417-49138152	K562	blood:	n/a	n/a
10	EP300	chr3:49135722-49135967	SK-N-SH_RA	brain:	n/a	n/a
11	ETS1	chr3:49135922-49136259	K562	blood:	n/a	n/a
12	JUND	chr3:49135894-49136289	K562	blood:	n/a	n/a
13	POLR2A	chr3:49135933-49136334	PFSK-1	brain:	n/a	n/a
14	EP300	chr3:49135916-49136284	K562	blood:	n/a	n/a
15	ETS1	chr3:49135781-49136328	K562	blood:	n/a	n/a
16	MXI1	chr3:49135937-49136381	K562	blood:	n/a	n/a
17	HDAC2	chr3:49135830-49136232	K562	blood:	n/a	n/a
18	TCF7L2	chr3:49135647-49136014	Hela-S3	cervix:	n/a	n/a
19	RFX5	chr3:49135955-49136189	K562	blood:	n/a	n/a
20	ATF1	chr3:49135870-49136267	K562	blood:	n/a	n/a
21	NR2F2	chr3:49135847-49136367	K562	blood:	n/a	n/a
22	TEAD4	chr3:49135828-49136372	K562	blood:	n/a	n/a
23	CBX3	chr3:49135821-49136346	K562	blood:	n/a	n/a
24	TBL1XR1	chr3:49135958-49136254	K562	blood:	n/a	n/a
25	ELF1	chr3:49135868-49136289	K562	blood:	n/a	n/a
26	MAX	chr3:49135755-49136331	K562	blood:	n/a	n/a
27	TAL1	chr3:49135857-49136357	K562	blood:	n/a	n/a
28	EGR1	chr3:49135956-49136493	K562	blood:	n/a	n/a
29	CEBPB	chr3:49135944-49136306	K562	blood:	n/a	n/a
30	FOXP2	chr3:49135815-49136261	PFSK-1	brain:	n/a	n/a
31	ZC3H11A	chr3:49135833-49136004	K562	blood:	n/a	n/a
32	GABPA	chr3:49135858-49136356	K562	blood:	n/a	n/a
33	REST	chr3:49135810-49136263	K562	blood:	n/a	n/a
34	BHLHE40	chr3:49135935-49136284	K562	blood:	n/a	n/a
35	GATA2	chr3:49135860-49136377	K562	blood:	n/a	n/a
36	HDAC2	chr3:49135916-49136263	K562	blood:	n/a	n/a
37	SIN3AK20	chr3:49135944-49136274	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr3:49135731-49136386	K562	blood:	n/a	n/a
39	MYC	chr3:49135903-49136330	K562	blood:	n/a	n/a
40	POLR2A	chr3:49135652-49136307	K562	blood:	n/a	n/a
41	RCOR1	chr3:49135933-49136380	K562	blood:	n/a	n/a
42	STAT5A	chr3:49135917-49136362	K562	blood:	n/a	n/a
43	MAX	chr3:49135889-49136226	K562	blood:	n/a	n/a
44	RCOR1	chr3:49135942-49136310	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49135631..49137925-chr3:49140087..49143203,4	MCF-7	breast:
2	chr3:49128926..49138937-chr3:49145476..49160975,31	K562	blood:
3	chr3:49134791..49138406-chr3:49156749..49159761,5	K562	blood:
4	chr3:49131736..49133437-chr3:49134322..49137083,2	MCF-7	breast:
5	chr3:49058895..49061376-chr3:49135583..49140082,4	MCF-7	breast:

No data

Variant related genes	Relation type
QRICH1	TF binding region
QARS	TF binding region
ENSG00000198218	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000172053	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10154895	0.85[ASN][1000 genomes]
rs10865954	0.90[ASN][1000 genomes]
rs11130182	0.83[ASN][1000 genomes]
rs11130184	0.87[ASN][1000 genomes]
rs1134591	0.84[EUR][1000 genomes]
rs11552724	0.95[ASN][1000 genomes]
rs11705737	0.83[EUR][1000 genomes]
rs11706052	0.82[ASN][1000 genomes]
rs11706189	0.85[ASN][1000 genomes]
rs11712006	0.95[ASN][1000 genomes]
rs11713297	0.85[ASN][1000 genomes]
rs11715581	0.87[ASN][1000 genomes]
rs11716334	0.87[ASN][1000 genomes]
rs11920534	0.81[EUR][1000 genomes]
rs11924597	0.81[EUR][1000 genomes]
rs12487580	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12490393	0.87[ASN][1000 genomes]
rs12491743	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12493001	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12629759	0.87[ASN][1000 genomes]
rs12636030	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12637037	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13064883	0.81[EUR][1000 genomes]
rs13064911	0.83[EUR][1000 genomes]
rs13072554	0.82[ASN][1000 genomes]
rs13072911	0.81[EUR][1000 genomes]
rs13076394	0.83[EUR][1000 genomes]
rs13080725	0.82[ASN][1000 genomes]
rs13315711	0.84[EUR][1000 genomes]
rs13316620	0.84[EUR][1000 genomes]
rs3212	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34326553	0.95[ASN][1000 genomes]
rs34580506	0.95[ASN][1000 genomes]
rs34889065	0.95[ASN][1000 genomes]
rs35108630	0.82[ASN][1000 genomes]
rs35283189	0.95[ASN][1000 genomes]
rs35673421	0.95[ASN][1000 genomes]
rs36133651	0.84[EUR][1000 genomes]
rs3923475	0.82[ASN][1000 genomes]
rs4072859	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4279134	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308307	0.87[ASN][1000 genomes]
rs4364202	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4499638	0.82[ASN][1000 genomes]
rs4513485	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4521268	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536858	0.82[ASN][1000 genomes]
rs4955410	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4955418	0.82[ASN][1000 genomes]
rs4955419	0.87[ASN][1000 genomes]
rs4955420	0.87[ASN][1000 genomes]
rs4974080	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4974082	0.84[EUR][1000 genomes]
rs4974091	0.83[EUR][1000 genomes]
rs5030795	0.95[ASN][1000 genomes]
rs55713230	0.82[ASN][1000 genomes]
rs61583136	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62262517	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6414613	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6446196	0.84[EUR][1000 genomes]
rs6446198	0.82[EUR][1000 genomes]
rs6446205	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66991555	0.90[ASN][1000 genomes]
rs6768433	0.80[EUR][1000 genomes]
rs6770112	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6779394	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781790	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6784111	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6786665	0.83[EUR][1000 genomes]
rs6789285	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6790914	0.82[ASN][1000 genomes]
rs6791234	0.82[EUR][1000 genomes]
rs6795025	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7373790	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7430198	0.81[EUR][1000 genomes]
rs7431710	0.80[EUR][1000 genomes]
rs7432989	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7612459	0.83[EUR][1000 genomes]
rs7615235	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621015	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7626445	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628719	0.84[EUR][1000 genomes]
rs7632267	0.82[EUR][1000 genomes]
rs7636057	0.84[EUR][1000 genomes]
rs7643368	0.83[EUR][1000 genomes]
rs7645551	0.86[EUR][1000 genomes]
rs8926	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9683094	0.82[AMR][1000 genomes]
rs9814987	0.90[ASN][1000 genomes]
rs9835439	0.85[ASN][1000 genomes]
rs9837237	0.87[ASN][1000 genomes]
rs9837625	0.87[ASN][1000 genomes]
rs9840050	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846123	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9850134	0.83[EUR][1000 genomes]
rs9855123	0.85[ASN][1000 genomes]
rs9862483	0.85[ASN][1000 genomes]
rs9867373	0.82[EUR][1000 genomes]
rs9880088	0.85[ASN][1000 genomes]
rs9884022	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs13064784	WDR6	cis	Artery Tibial	GTEx
rs13064784	NICN1	cis	Thyroid	GTEx
rs13064784	NCKIPSD	cis	Muscle Skeletal	GTEx
rs13064784	NCKIPSD	cis	Whole Blood	GTEx
rs13064784	AMT	cis	Artery Aorta	GTEx
rs13064784	WDR6	cis	Whole Blood	GTEx
rs13064784	WDR6	cis	Esophagus Muscularis	GTEx
rs13064784	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs13064784	WDR6	cis	lung	GTEx
rs13064784	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs13064784	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs13064784	WDR6	cis	Muscle Skeletal	GTEx
rs13064784	WDR6	cis	Adipose Subcutaneous	GTEx
rs13064784	CCDC36	cis	Artery Tibial	GTEx
rs13064784	WDR6	cis	Esophagus Mucosa	GTEx
rs13064784	NCKIPSD	cis	Nerve Tibial	GTEx
rs13064784	WDR6	cis	Heart Left Ventricle	GTEx
rs13064784	AMT	cis	Thyroid	GTEx
rs13064784	AMT	cis	Whole Blood	GTEx
rs13064784	NICN1-AS1	cis	Thyroid	GTEx
rs13064784	WDR6	cis	Nerve Tibial	GTEx
rs13064784	ARIH2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49132400-49136000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:49132400-49136800	Weak transcription	Fetal Brain Male	brain
3	chr3:49132400-49136800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:49132400-49140800	Weak transcription	Right Atrium	heart
5	chr3:49132400-49141600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:49132800-49136400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:49132800-49136400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:49133000-49136000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:49133000-49140000	Strong transcription	HSMMtube	muscle
10	chr3:49133000-49140200	Strong transcription	NHLF	lung
11	chr3:49133000-49140400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:49133000-49140400	Strong transcription	Right Ventricle	heart
13	chr3:49133000-49140600	Strong transcription	Fetal Muscle Leg	muscle
14	chr3:49133000-49140600	Strong transcription	Osteobl	bone
15	chr3:49133000-49140800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:49133000-49140800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:49133000-49140800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:49133000-49140800	Strong transcription	Fetal Intestine Small	intestine
19	chr3:49133000-49140800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr3:49133000-49140800	Strong transcription	Placenta	Placenta
21	chr3:49133000-49140800	Strong transcription	Fetal Stomach	stomach
22	chr3:49133200-49137400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:49133200-49140000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:49133200-49140000	Strong transcription	Liver	Liver
25	chr3:49133200-49140200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:49133200-49140200	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:49133200-49140200	Strong transcription	Adipose Nuclei	Adipose
28	chr3:49133200-49140200	Strong transcription	Lung	lung
29	chr3:49133200-49140400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:49133200-49140600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:49133200-49140600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:49133200-49140600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:49133200-49140600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:49133200-49140600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:49133200-49140600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:49133200-49140600	Strong transcription	Fetal Intestine Large	intestine
37	chr3:49133200-49140600	Strong transcription	Fetal Thymus	thymus
38	chr3:49133200-49140600	Strong transcription	Stomach Smooth Muscle	stomach
39	chr3:49133200-49140800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:49133200-49140800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:49133200-49140800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:49133200-49140800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:49133200-49141000	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:49133200-49141000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:49133200-49141000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:49133200-49141000	Strong transcription	Brain Cingulate Gyrus	brain
47	chr3:49133200-49141200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:49133400-49136800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:49133400-49140200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr3:49133400-49140400	Strong transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links